Chapter 2 – Basic Chemistry/Biochemistry in Microbiology
Relevance to Microbiology:
Microbes are made of the same chemical components as all life. Understanding atoms,
bonds, and reactions helps explain microbial structure, metabolism, and how microbes
cause disease or are targeted by drugs.
Atoms & Bonds
o Atoms = basic unit of matter.
o Bonds: covalent (strong, share e⁻), ionic (transfer e⁻, weaker in water), hydrogen
bonds (important in water, DNA, proteins).
Water & pH
o Water is polar → solvent for life, critical for biochemical reactions.
o pH affects microbial growth (acidophiles, neutrophiles, alkaliphiles).
Macromolecules
o Carbohydrates: energy (glucose), structural (peptidoglycan).
o Lipids: membranes, energy storage, endotoxins (lipid A in Gram-negative).
o Proteins: enzymes, transport, structure.
o Nucleic acids: genetic information (DNA, RNA).
Biochemical Context:
Understanding microbial macromolecules is essential for developing stains, antibiotics,
and growth media.
Chapter 3 – Microscopy & Staining
Microscopy Types
o Light Microscopy: brightfield, darkfield, phase-contrast, fluorescence.
o Electron Microscopy: TEM (internal structures), SEM (surface details).
o Use in microbiology: visualization, diagnosis, structural analysis.
Staining
o Increases contrast between microbes and background.
o Gram Stain: differential stain distinguishing cell wall types.
Gram-positive: purple (thick peptidoglycan).
Gram-negative: pink/red (thin peptidoglycan + outer membrane).
o Endospore Stain: highlights resistant structures; spores stain green, cells stain
red/pink.
Chapter 4 – Prokaryotic Cell Structure & Function
Cell Wall
o Peptidoglycan: repeating disaccharides + polypeptides → structural support.
o Gram-positive: thick PG, teichoic acids.
o Gram-negative: thin PG, outer membrane with lipopolysaccharide (LPS →
endotoxin).
Gram Staining Mechanism (Fig. 4.13)
o Crystal violet + iodine form complex → retained in thick PG (Gram+).
o Alcohol dissolves outer membrane & thin PG can’t hold dye (Gram–).
o Safranin counterstains Gram– cells pink.
Lysozyme & Antibiotics
o Lysozyme hydrolyzes PG bonds → damages cell wall.
o Penicillin prevents PG synthesis.
Plasma Membrane
o Selectively permeable phospholipid bilayer.
o Functions: transport, ATP production, enzyme location.
Biofilms & Adherence
o Biofilms = microbial communities encased in slime/glycocalyx, resist
antimicrobials.
o Glycocalyx: capsule (organized, protective) or slime layer (loose, sticky).
o Adherence: microbes attach via fimbriae, glycocalyx → key in infection.
Endospores
o Dormant, highly resistant structures (heat, chemicals, desiccation).
o Ensure survival in harsh conditions.
o Medical relevance: Clostridium, Bacillus.
Endotoxins vs. Exotoxins (Ch. 15)
o Exotoxins: proteins secreted by Gram+ and Gram–; specific targets, highly toxic.
o Endotoxins: LPS (lipid A) in Gram– outer membrane; released on cell lysis;
systemic effects (fever, shock).
Chapter 5 – Microbial Metabolism
Metabolism Overview
o All chemical reactions in a cell.
o Balance between catabolism (energy release, breakdown) and anabolism
(biosynthesis).
o Essential for growth, survival, pathogenesis.
Enzymes
o Biological catalysts, lower activation energy.
o Sensitive to temperature, pH, inhibitors (antibiotics).
Energy Production
o ATP: energy currency.
o Generated via substrate-level phosphorylation, oxidative phosphorylation,
photophosphorylation.
Carbohydrate Catabolism
o Glycolysis: glucose → pyruvate, produces small ATP & NADH.
o TCA Cycle: oxidizes acetyl-CoA → CO₂, generates NADH, FADH₂.
o Oxidative Phosphorylation: electron transport chain → ATP via proton gradient.
Respiration & Fermentation (Table 5.5)
o Aerobic Respiration: final e⁻ acceptor = O₂ → high ATP yield.
o Anaerobic Respiration: final e⁻ acceptor = inorganic molecule (NO₃⁻, SO₄²⁻,
CO₃²⁻).
o Fermentation: organic molecules as e⁻ acceptors, low ATP, produces
acids/alcohols.
Metabolic Diversity (Fig. 5.28)
o Organisms classified by energy & carbon source (photoautotrophs,
chemoheterotrophs, etc.).
Biochemical Tests (Figs. 5.22, 5.24, 5.33)
o Identify unknown bacteria by metabolic properties.
o Examples: fermentation tests, enzyme activity, selective media.
o Basis for lab identification of bacterial unknowns.
Chapter 6 – Microbial Growth
Bacterial Growth
o Increase in cell number, not size.
o Requires nutrients, energy, favorable environment.
Growth Phases (log representation)
o Lag phase: adjustment, little division.
o Log phase: exponential growth, highest metabolic activity, best for antibiotics.
o Stationary phase: nutrient depletion, waste accumulation, balance between
growth & death.
o Death phase: cell death exceeds growth.
Table 6.1
o Summarizes physical/chemical requirements for growth (temp, pH, osmotic
pressure, O₂ availability, nutrients).